Chapter 6

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Repeating values of  and  make up predictable orientations of amino acid with a chain, this predictable orientation forms A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

H

The strength of comes from close packing of glycine residues and the characteristics of hydroxyproline allowing formation of a left- handed helical conformation which combines with two other left handed structures to form a right-handed triplet helix. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

I

The overall arrangement of the regular structural elements such as the α helix and the β sheet in the protein are considered the protein's A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

A

A historical experiment exploring denaturation upon β- mercaptoethanol reduction of disulfide bonds and spontaneous renaturation upon dialysis to remove the β- mercaptoethanol was carried out using the protein . This experiment demonstrated the importance of disulfide bonds and amino acid sequence in folding of proteins. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

K Signup and view all the answers

A rigid, planar structure between at least two amino acids consisting of about 40% double bond character is characteristic of a A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

J Signup and view all the answers

The of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

D Signup and view all the answers

is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which forms an α helix with one hydrophobic side. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

B Signup and view all the answers

In most peptide groups the conformation is not sterically favored. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

EF Signup and view all the answers

In vivo protein folding is often is assisted by A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

C Signup and view all the answers

In a , the  and  angles of the peptide backbone would orient atoms closer than their van der Waals distance. A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha

G Signup and view all the answers

In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of  and  that are allowed in rather than in because there is greater opportunity for separation of amino acid side chains.

β sheet…α helix Signup and view all the answers

In a protein, the most conformationally restricted amino acid is ; the least conformationally restricted is .

Pro, Gly Signup and view all the answers

Which of the following has (have) both a favorable hydrogen bonding pattern and  and  values that fall within the allowed Ramachandran conformational regions?

all of the above Signup and view all the answers

Which one of these characteristics is not true for the  helix?

There is a requirement for glycine every third amino acid residue. Signup and view all the answers

Which of these characteristics does not describe the  sheet?

Parallel  sheets containing fewer than five chains are the most common. Signup and view all the answers

Which statement below does not describe fibrous proteins?

Domains have a globular fold. Signup and view all the answers

Which of the following changes would not alter the functional characteristics of α keratin?

All of the above would alter the functional characteristics of keratin. Signup and view all the answers

Which of the following statements is true regarding collagen?

The requirement for glycine every 3rd amino acid is essential for the triplet helix formation. Signup and view all the answers

Which of the following gives the best example of a nonrepetitive structure in a protein?

a 13 residue α helix with a Gln at position n+12 which hydrogen bonds to a residue at position n+10 Signup and view all the answers

Which of the following is true regarding crystalline proteins?

A and B are true. Signup and view all the answers

In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:

scurvy Signup and view all the answers

Of the following, which amino acid is most likely to be found in position 1 or 4 on α keratin?

Ala Signup and view all the answers

Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein?

Glu and Lys Signup and view all the answers

The low pH found in the gut can enhance the digestibility of dietary protein by causing

protein denaturation Signup and view all the answers

Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation?

aggregation of hydrophobic regions in the protein Signup and view all the answers

Imagine that a researcher treated a protein with a high concentration of a chaotropic agent. Which of the following is the most likely result of the treatment? I. Nonpolar portions of the protein become more soluble. II. The protein begins to denature , III. The protein stability increases due to hydrophobic collapse,

I,II Signup and view all the answers

For -sheets, the terms ‘parallel’ and ‘antiparalllel’ refer to

the ‘direction’ of the associated peptide strands Signup and view all the answers

In general molecular chaperone proteins function by

preventing premature folding by binding hydrophobic regions of the protein. Signup and view all the answers

Conventional one dimensional NMR spectroscopy is not generally an effective tool for determination of protein structure because… I. Proteins (including small proteins) have a high number of hydrogen atoms. II. NMR requires a high quality protein crystal. III. The NMR spectra exhibit high peak overlap.

I and III Signup and view all the answers

When comparing similarities among multiple protein structures, which of the following is false?

Proteins with the same function from different species are likely to be more similar in sequence than in structure. Signup and view all the answers

The structure and sequence of a protein of unknown function was examined. Which of the following provides the best prediction of the protein's function?

the observation of motif known as the Rossmann fold. Signup and view all the answers

The Protein Data Bank (PDB) is a database provides structural information about proteins that may be useful for which of the following? I. A researcher studying the changes in protein fold associated with prions. II. A researcher classifying structural elements by function. III A researcher designing a compound to bind tightly to a particular region in the protein.

I, II, III Signup and view all the answers

Noncovalent forces that stabilize protein structure include all of the following except .

disulfide bridges Signup and view all the answers

The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that

1° structure can determine 3° structure Signup and view all the answers

The first step in the folding of disordered polypeptides into ordered functional protein is the formation of _.

2° structure Signup and view all the answers

Evolutionary processes have

enhanced efficient folding pathways. Signup and view all the answers

Chaperonins such as the GroEL/ES system

require ATP hydrolysis. Signup and view all the answers

Protein diseases can be caused by which of the following

All of the above are potential causes. Signup and view all the answers

Which of the following would be most stable based on the information you have learned about protein structure?

a β sheet region made up of amino acids Val, Ile, Phe Signup and view all the answers

Hydrogen bonds and maximum separation of amino acid side chains make the very stable and energetically

α helix and β sheet, favorable Signup and view all the answers

A chaperonin

helps fold some proteins in their lowest energy state. Signup and view all the answers

A helix has hydrogen bonds between the carbonyl group from residue “n” and the amino group of residue “n+6,” which of the following is TRUE?

It has more residues per turn than an α helix. Signup and view all the answers

Which of the following contribute to the minimization of energy that occurs with protein folding?

orientating amino acid groups to maximize hydrogen bonding Signup and view all the answers

Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)?

aggregation of a misfolded protein. Signup and view all the answers

Proteins can denature due to a change in

all of the above Signup and view all the answers

Examine the three sequences below for collagen-like proteins. If hydrogen bonding were the most important feature in determining strength in fibrous proteins, which of the following sequences likely has the highest melting temperature and why? (Note: Flp = fluoroproline; Hyp = hydroxyproline) I. Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly II. Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly III. Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr

“1” because Hyp has OH groups Signup and view all the answers

Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)? Val – Cys – Lys – Val - Cys – Ala – Cys - Val – Cys – Lys – Val - Cys – Ala – Cys

 keratin Signup and view all the answers

Which of the following structural proteins has the greatest elasticity?

pleated collagen Signup and view all the answers

Noncovalent interactions account for the strength of which of the following structural proteins?

collagen Signup and view all the answers

Examine the three sequences below for collagen-like proteins and their melting temperatures (Tm). (Note: Flp = fluoroproline; Hyp = hydroxyproline) Based on this data, what is the most important feature in determining the strength of the collagen protein?

…-Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly-… Tm=60 C o

…-Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly-… Tm=78 C o

…-Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr-… Tm=30 C

inductive effect Signup and view all the answers

When considering fibrous proteins, which of the following statements is TRUE?

Noncovalent interactions contribute to the strength of all of these proteins. Signup and view all the answers

In a Ramachandran diagram the region representing the angles of  and  that correspond to those commonly made by an amino acid that favors a left-handed  helix are different from those angles commonly made by an amino acid that favors right-handed  helix formation. Which of the following statements provides a plausible explanation for this difference?

Groups which would normally undergo high steric hindrance in the right-handed arrangement are separated maximally in the left-handed arrangement. Signup and view all the answers

Which of the characteristics of collagen structure listed below contrubute to the tensi le strength of collagen? I. Collagen is made up of a triplet helix where 3 left-handed helices twist together in a right handed sense. II. Collagen includes at repeating sequence of amino acids with glycine every 3 amino acids in a helix with about 3 amino acids per turn. III. The three left-handed helices are staggered to allow close packing between glycine residues and rigidity from the bulky and inflexible proline/hydroxyproline.